FIAS Scientific Report 2011 - Frankfurt Institute for Advanced Studies ...

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Structure and dynamics of clusters and fullerenes Collaborators: A.V. Solov’yov 1 , A.V. Korol 1 , A.V. Verkhovtsev, 1 R.G. Polozkov 2 , V.K. Ivanov 2 1 Frankfurt Institute for Advanced Studies, 2 St. Petersburg State Polytechnic University, Russia A self-consistent Hartree-Fock calculation of electronic structure of noble gas endohedral fullerenes A@C60 was carried out for the first time [1,2]. All electrons of the encaged atom and 240 delocalized electrons of C60 were considered simultaneously within unified electronic configuration. It was shown [3,4] that the account of the non-local exchange interaction within the Hartree-Fock approximation leads to the significant modification of the 3p and 4d shells as opposed to the local exchange interaction within the local density approximation. As a result of the modification the redistribution of the electronic density of the 3p and 4d shells appears and causes the accumulation of the additional positive charge in the vicinity of the encaged atom and the additional negative charge on the fullerene core. Related publications in 2011: �� Figure: The 3p wave function in free Ar atom (solid line), in pristine C60 (dashed line) and in Ar@C60 calculated within the HF approximation (line with triangles) and the LDA (filled-circled line). Results of the LDA calculation performed by Madjet et al. (2007) are also presented (open-circled line). 1. A.V. Verkhovtsev, R.G. Polozkov, V.K. Ivanov, A.V. Korol, A.V. Solov’yov, Investigation of electronic structure of noble gas endohedral fullerenes, Science and Technology Bulletin of Saint Petersburg State Polytechnic University, issue No 1(116), 61-70 (2011) (in Russian). 2. A.V. Verkhovtsev, R.G. Polozkov, V.K. Ivanov, A.V. Korol, A.V. Solov’yov, Self-consistent Hartree-Fock approach to electronic structure of endohedral fullerenes, International Conference ‘Advanced Carbon Nanostructures (ACN 2011)’ Book of Abstracts, p. 311 (St. Petersburg, Russia, July 4-8, 2011). 3. A.V. Verkhovtsev, R.G. Polozkov, V.K. Ivanov, A.V. Korol, A.V. Solov’yov, Role of Exchange Interaction in Self-Consistent Calculations of Endohedral Fullerenes, Nucl. Instrum. Meth. B, in press (2011) (see also arXiv:1108.0918). 4. A.V. Verkhovtsev, R.G. Polozkov, V.K. Ivanov, A.V. Korol, A.V. Solov’yov, Self-consistent description of endohedral fullerenes’ electronic structure within the Hartree-Fock and the local density approximations, The Fifth International Symposium ‘Atomic Cluster Collisions (ISACC 2011)’ Book of Abstracts, p. 76 (Berlin, Germany, July 20-25, 2011). 92 �
DNA unzipping Collaborators: S.N. Volkov 1 , E.V. Paramonova 2 , A.V. Yakubovich 3 , A.V. Solov’yov 3 1 Bogolyubov Institute for Theoretical Physics, Ukraine, 2 Institute of Mathematical Problems of Biology RAS, Russia, 3 Frankfurt Institute for Advanced Studies Short description: All-atom molecular dynamics (MD) simulations of DNA duplex unzipping in a water environment were performed. The investigated DNA double helix consists of a Drew-Dickerson dodecamer sequence and a hairpin (AAG) attached to the end of the double-helix chain. The considered system is used to examine the process of DNA strand separation under the action of an external force. This process occurs in vivo and now is being intensively investigated in experiments with single molecules. Main results: • The DNA dodecamer duplex is consequently unzipped pair by pair by means of the steered MD. The unzipping trajectories turn out to be similar for the duplex parts with G·C content and rather distinct for the parts with A·T content. • It is shown that during the unzipping each pair experiences two types of motion: relatively quick rotation together with all the duplex and slower motion in the frame of the unzipping fork. In the course of opening, the complementary pair passes through several distinct states: (i) the closed state in the double helix, (ii) the metastable preopened state in the unzipping fork and (iii) the unbound state. • The performed simulations show that water molecules participate in the stabilization of the metastable states of the preopened base pairs in the DNA unzipping fork. Related publications in 2011: Figure 1. DNA duplex constructed from a Drew-Dickerson dodecamer with hairpin AAG: (a) nucleotide content in DD-h; (b) additional external force applied to the opposite phosphate groups of different strands (shown by red spheres) that drives the directed unzipping process of dsDNA. Figure 2. Base stretching coordinate (in angstrom) and the number of water molecules that link the bases in the unzipping pair. 1. S.N. Volkov, E.V. Paramonova, A.V. Yakubovich, A.V. Solov’yov, Micromechanics of base pair unzipping in the DNA duplex, J. Phys.: Condens. Matter 24 035104 (2012). 93
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FIAS Scientific Report 2011
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FIAS Scientific Report 2011 Table o
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Physics Research highlights 2011 To
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1. Partner Research Centers 9
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ExtreMe Matter Institute EMMI by Ca
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Bernstein Focus Neurotechnology Fra
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2. Graduate Schools 15
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participants reported on their proj
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Courses offered at FIGSS Summer Sem
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3. FIAS Scientific Life 21
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28.07.2011 Prof. Dr. Victor Flambau
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Conferences and meetings (co)organi
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4. Research Reports 4.1 Nuclear Phy
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Hydrodynamics of a quark droplet Co
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Production of hyper-nuclei in react
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On production and properties of mul
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Monte Carlo modeling microdosimetry
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Monte Carlo simulation of the spall
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Dimuon radiation within a (3+1)d hy
Page 41 and 42: Initial state anisotropies and thei
Page 43 and 44: Chiral hadronic model including res
Page 45 and 46: Trace anomaly and the vector coupli
Page 47 and 48: Dileptons from the strongly interac
Page 49 and 50: Space-time evolution of the magneti
Page 51 and 52: Extreme isospin in heavy nuclei Col
Page 53 and 54: Production of heavy and superheavy
Page 55 and 56: The phase diagram in T -µB-Nc spac
Page 57 and 58: Critical Zeeman Fields for Unitary
Page 59 and 60: BCS-BEC Crossover in 2D Fermi Gases
Page 61 and 62: Applications of a chiral SU(3) mode
Page 63 and 64: The phase diagram of black holes in
Page 65 and 66: Black holes in short scale modified
Page 67 and 68: Fractal dimensions and micro-struct
Page 69 and 70: Untangling the interactions between
Page 71 and 72: Stimulus information coded by spike
Page 73 and 74: Non-stationarity of neuronal activi
Page 75 and 76: Timescale of information processing
Page 77 and 78: Discovery of agency in 6 and 8-mont
Page 79 and 80: Power spectra of the natural input
Page 81 and 82: Self-organization in recurrent neur
Page 83 and 84: Learning mechanisms underlying visu
Page 85 and 86: Emerging Bayesian priors in a self-
Page 87 and 88: Non-linear generative models and th
Page 89 and 90: Preference elicitation and Bayesian
Page 91: 4.3 Biology, Chemistry, Molecules,
Page 95 and 96: Statistical mechanics of protein fo
Page 97 and 98: Phase transitions in large clusters
Page 99 and 100: Photo-processes in fullerenes and e
Page 101 and 102: Assessment of complex DNA damage Co
Page 103 and 104: Novel light sources: Crystalline un
Page 105 and 106: Monte-Carlo code for channeling dyn
Page 107 and 108: Programs for many-body descriptions
Page 109 and 110: Are 12 C radiation effects in liver
Page 111 and 112: Objective identification of residue
Page 113 and 114: Structural basis for the dual RNA-r
Page 115 and 116: The ALICE High Level Trigger Collab
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The success of FIAS would not have
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